Cartridge interface module

ABSTRACT

A cartridge interface module (CIM), configured to engage with a removable microfluidic cartridge in a nucleic acid analyzer system can include a fluidics component, which is configured to initiate and support a liquid extraction of nucleic acids from a biological sample contained in the removable microfluidic cartridge. The CIM also includes a polymerase chain reaction (PCR) assembly component which can be configured to initiate and support amplification of the extracted nucleic acids. The CIM may also include a high voltage electrodes component that is configured to initiate and support separation of the amplified nucleic acids into nucleic acid fragments in a separation channel of the removable microfluidic cartridge. The CIM also includes a detection optics component that can be configured to collect, detect, and direct label nucleic acid fragments. The CIM is configured to integrate with a microfluidic chip architecture of an inserted removable microfluidic cartridge.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application No.61/805,729, filed on Mar. 27, 2013, the disclosure of which isincorporated in its entirety by reference herein.

BACKGROUND

Genetic testing is used for various purposes, includingforensic/identity testing, paternity testing, diagnostic testing,disease screening, environmental monitoring, food safety etc. Genetictesting relies on being able to analyze nucleic acids in a biologicalsample. Accordingly, improvements in nucleic acid analysis will furtherenhance the utility of genetic testing. In humanidentification-applications of genetic testing, such as forensicapplications, nucleic acid analysis can be used to provide near certainmatching of a biological sample to a person.

SUMMARY

In embodiments, a cartridge interface module (CIM), configured to engagewith a removable microfluidic cartridge in a nucleic acid analyzersystem can include a fluidics component, which is configured to initiateand support a liquid extraction of nucleic acids from a biologicalsample contained in the removable microfluidic cartridge. The CIM alsoincludes a polymerase chain reaction (PCR) assembly component, which isconfigured to initiate and support amplification of the extractednucleic acids. The CIM can also include a high voltage electrodescomponent, which is configured to initiate and support separation of theamplified nucleic acids into nucleic acid fragments in a separationchannel of the removable microfluidic cartridge. The CIM also includes adetection optics component, which is configured to detect labelednucleic acid fragments. The CIM is configured to integrate with amicrofluidic chip architecture of an inserted removable microfluidiccartridge for execution of the extraction, amplification, and separationof the biological sample within the removable microfluidic cartridge.

In embodiments, a method of analyzing a biological sample for DNAanalysis can include receiving a removable microfluidic cartridge into aCIM of a nucleic acid analyzer system. The method also includesinitiating and supporting extraction of nucleic acids from thebiological sample contained within the removable microfluidic cartridge,via a fluidics component of the CIM while engaged with the removablemicrofluidic cartridge. The method can also include initiating andsupporting amplification of the extracted nucleic acids, via apolymerase chain reaction assembly component of the CIM while engagedwith the removable microfluidic cartridge. The method may also includeinitiating and supporting separation of the amplified nucleic acids intonucleic acid fragments, via a high voltage electrodes component of theCIM while engaged with a separation channel of the removablemicrofluidic cartridge. The method also includes directing an inputlight beam into a separation channel for detection and collection of thenucleic acid fragments, via a detection optics component of the CIM.

In embodiments, a CIM of a nucleic acid analyzer system may include afluidics component, a high voltage electrode component, a pneumaticconnector component, a cartridge support component, a microfluidic valveactuator component, a liquid extraction heater component, a detectionoptics component, a stage heater component, and a polymerase chainreaction component. The components of the CIM are configured tointegrate with a microfluidic chip architecture of an inserted removablemicrofluidic cartridge to extract, amplify, and separate a biologicalsample within the removable microfluidic cartridge.

BRIEF DESCRIPTION OF THE DRAWINGS

Various exemplary embodiments will be described in detail with referenceto the following figures, wherein:

FIG. 1 is a block diagram of an exemplary nucleic acid analyzer;

FIG. 2 is a conceptual diagram of the functions performed by embodimentsof the microfluidic cartridge;

FIG. 3 shows exemplary features for performing nucleic acid extraction;

FIG. 4 shows a plurality of exemplary sample acceptors fluidicallycoupled to an exemplary microfluidic cartridge;

FIG. 5 shows another view of the plurality of exemplary sample acceptorsfluidically coupled to the exemplary microfluidic cartridge shown inFIG. 4;

FIG. 6 shows a portion of an exemplary nucleic acid analyzer thatincludes an extraction thermal module;

FIG. 7 shows exemplary features for performing nucleic acidamplification;

FIG. 8 shows exemplary features of a loadable reservoir;

FIG. 9 shows exemplary features for performing nucleic acid separation;

FIG. 10 shows an exemplary microfluidic cartridge and an exemplarysealing layer to be applied over at least a major portion of themicrofluidic cartridge;

FIG. 11 shows an exemplary frangible seal within a fluidic channel;

FIG. 12 is a schematic of an exemplary microfluidic cartridge thatcombines various features for nucleic acid extraction, nucleic acidamplification, and nucleic acid separation;

FIG. 13 is an illustration of a cartridge interface module;

FIG. 14 is a drawing of a cartridge interface module;

FIG. 15 is a drawing of a pyrometer used with a cartridge interfacemodule; and

FIG. 16 is a flow chart illustrating an exemplary process of analyzing abiological sample.

DETAILED DESCRIPTION

FIG. 1 shows a block diagram of an exemplary nucleic acid analyzer 100.As shown, the nucleic acid analyzer 100 can include a microfluidiccartridge module 105, a cartridge interface module 104, an extractionthermal module 110, an amplification thermal module 115, a pressuremodule 120, a high voltage module 125, a detection module 130, a powermodule 135, a computing module 140, and a controller module 145. Themodules can be operably connected as shown in FIG. 1. In embodiments,the modules can also be combined or more than one of each module may bepresent in a nucleic acid analyzer.

The nucleic acid analyzer 100 is capable of performing nucleic acidanalysis using a microfluidic cartridge. The nucleic acid analyzer 100can be operated to perform nucleic acid analysis by a user without theneed for substantial experience with and knowledge of the processes usedto perform nucleic acid analysis. For example, the appropriateprocedures for using the nucleic acid analyzer 100 can be learned in anhour or less. The nucleic acid analyzer 100 is designed to use liquidvolumes on the order of micro-liters or less. By using micro-literliquid volumes, nucleic analysis can be performed in reduced time ascompared to time-intensive nucleic acid analysis currently in use. Inembodiments, nucleic acid analysis can be performed in less than twohours.

The microfluidic cartridge module 105 is configured to accept one ormore microfluidic cartridges (not shown). The cartridge interface module104 is configured to operably couple the microfluidic cartridge module105 to the other modules. In an embodiment, some of the other modules,such as the detection module 130, the extraction thermal module, theamplification thermal module 115, and the like, can be integrated in thecartridge interface module 104. The microfluidic cartridge can include amicro-to-macro interface and features that allow the microfluidiccartridge to be acted upon by other components of the nucleic acidanalyzer 100. The microfluidic cartridge can be a disposable cartridge,such as a single-use cartridge. In general, microfluidic cartridges caninclude various features for performing any of nucleic acid extraction,nucleic acid amplification, and nucleic acid separation. Defined withinthe microfluidic cartridge is a fluidic network formed from fluidicchannels, fluidic chambers and/or reservoirs, and other features forperforming nucleic acid extraction, nucleic acid amplification, and/ornucleic acid separation. The microfluidic cartridge can be constructedfrom any suitable material. As examples, the microfluidic cartridge canbe constructed from a plastic, polymeric material, glass, and the like.Additionally, the microfluidic cartridge can be constructed frommultiple types of materials.

The extraction thermal module 110 is configured to impart suitabletemperatures for nucleic acid extraction. The extraction thermal module110 can be controlled by the controller module 145. The extractionthermal module 110 can be coupled to a cartridge or a sample acceptorduring nucleic acid extraction. The extraction thermal module 110 canperform contact and/or non-contact thermal heating. In an example, theextraction thermal module 110 includes one or more contact heatingunits. Heating with the extraction thermal module can facilitate theextraction of nucleic acids with thermophilic enzymes.

The amplification thermal module 115 is configured to impart suitabletemperatures to the microfluidic cartridge during nucleic acidamplification. The amplification thermal module 115 can be controlled bythe controller module 145. In embodiments, the amplification thermalmodule 115 can be configured to impart thermal gradients and performtemperature sensing in a thermal cycling process in an amplificationchamber of the microfluidic cartridge. The amplification thermal module115 can perform contact and/or non-contact thermal heating. In anexample, the amplification thermal module 115 includes a non-contactheating unit, such as an infrared light source. The infrared lightsource can be a halogen light bulb. Further, the amplification thermalmodule 115 can include a temperature sensing unit. In an embodiment, thetemperature sensing unit is an infrared pyrometer that measuresblackbody radiation to determine the temperature of a selected portionof the microfluidic cartridge. Further, in embodiments, a single thermalmodule can be configured to impart temperature changes for bothextraction and amplification, as necessary, using the same heatingmeans.

The pressure module 120 is operably coupled to the microfluidiccartridge by, for example, the micro-to-macro interface. The pressuremodule 120 can be controlled by the controller module 145. The pressuremodule 120 is configured to provide pressures and/or vacuums (i.e.,positive and/or negative pressures) to the microfluidic cartridge tomove fluid within a fluidic network of the microfluidic cartridge. Inother words, the pressure module 120 can effectuate hydrodynamicmovement using, for example, pneumatic pressure in the microfluidiccartridge. In an embodiment, the pressure module 120 is coupled to oneor more clusters of vent ports on the microfluidic cartridge at themicro-to-macro interface. The pressure module 120 can connect a solenoidmanifold to the plurality of vent ports of the microfluidic cartridge atthe micro-to-macro interface. The pressure module 120 can impartpressure to each vent port independently to move fluid through thefluidic network in the microfluidic cartridge. In an embodiment, themicrofluidic cartridge has one or more valves that are configured to beactuated by the pressure module 120. The pressure module 120 can includea pressure/vacuum system, such as a pneumatic pressure/vacuum system, tosuitably control hydrodynamic movement in the fluidic network of themicrofluidic cartridge.

The power module 135 generates various operation powers for variouscomponents of the nucleic acid analyzer 100. In an example, the nucleicacid analyzer 100 is implemented using a modular design. Each module ofthe nucleic acid analyzer 100 requires an operation power supply, whichcan be different from the other modules. The power module 135 canreceive an AC power input, such as 100-240 V, 50-60 Hz, single phase ACpower from a power outlet. The power module 135 can use the AC powerinput to generate 5 V, 12 V, 24 V, and the like, to provide operationpowers for the various components of the nucleic acid analyzer 100. Inother embodiments, the power module 135 can be a battery.

The power module 135 also imparts power to the high voltage module 125as required for nucleic acid processes on the microfluidic cartridge,such as electrophoretic separation. The power module 135 can implementvarious protective functions, such as power outage protection, gracefulshut-down, and the like, to protect the various components and dataagainst power failure. In an embodiment, the power module 160 includes aback-up power, such as a battery module, to support one or moreprotective functions, such as graceful shut-down.

The high voltage module 125 receives power from the power module 135 andgenerates high voltages such as 1000 V, 2000 V, and the like, requiredfor nucleic acid processes on the microfluidic cartridge, such aselectrophoretic separation. The high voltage module 125 can apply thehigh voltages to the microfluidic cartridge under control of thecontroller module 145. For example, the high voltage module 125 includesan interface that applies the high voltages to electrodes on themicrofluidic cartridge to induce electro-kinetic injection and/orelectrophoretic separation.

The detection module 130 includes components configured to detectlabeled or dyed nucleic acids. The detection module 130 can becontrolled by the controller module 145. In an embodiment, the detectionmodule 130 is configured for fluorescence detection, such as multicolorfluorescence detection. The detection module 130 can include a lasersource unit, an optical unit, and a detector unit. The optical unitincludes a set of optics. In an embodiment, the optical unit includes aself-calibrating array of confocal optical components. The laser sourceunit emits a laser beam. In an example, the laser source unit includesan argon-ion laser unit. In another example, the laser source unitincludes a solid state laser, such as a coherent sapphire opticallypumped semiconductor laser unit. The solid state laser has theadvantages of reduced size, weight and power consumption.

In operation, the set of optics can direct the laser beam to penetrate adetection region of a separation channel in the microfluidic cartridge.The laser beam can excite fluorescent molecules attached to nucleicacids to emit fluorescence. The set of optics can then collect anddirect the emitted fluorescence to the detector unit for detection. Thedetector unit can convert the detected fluorescence into data forsubsequent processing by the computing module 140. An exemplarydetection technique is disclosed by co-pending U.S. application Ser. No.13/273,947 entitled, “Micro Fluidic Optic Design,” which is herebyincorporated herein by reference in its entirety.

The computing module 140 includes computing and communication units. Thecomputing module 140 is operably coupled to the controller module 145.The computing module 140 can provide a user interface. The userinterface can provide the status of the nucleic acid analyzer 100 andcan receive user instructions for controlling the operation of thenucleic acid analyzer 100. The computing module 140 includes variousstorage media to store software instructions and data. The computingmodule 140 can include nucleic analysis software that can perform dataprocessing based on raw data obtained from the detection module 130. Inaddition, the computing module 140 can be coupled to external processingunits, such as a database, a server, and the like to further process thedata obtained from nucleic acid analysis.

The controller module 145 can receive status signals and feedbacksignals from the various components and provide control signals to thevarious components according to a nucleic acid analysis procedure. Inaddition, the controller module 145 can provide the status signals tothe computing module 140 to inform a user of the status of nucleic acidanalysis. Further, the controller module 145 can receive userinstructions from the computing module 140 and can provide controlsignals to the various components based on user instructions.

FIG. 2 shows a conceptual diagram of the functions performed byembodiments of the microfluidic cartridge. The microfluidic cartridgeincludes various features for performing nucleic acid extraction 210,nucleic acid amplification 220, and/or nucleic acid separation 230.Nucleic acids include DNA and RNA. In an example, extraction,amplification, and separation are performed solely to analyze DNA. Inanother example, RNA is analyzed by, for example, extracting RNA,reverse transcribing RNA and amplifying the resulting cDNA, andseparating the DNA. Importantly, in embodiments, no additionalpurification feature is required between features for performing nucleicacid extraction 210 and nucleic acid amplification 220.

Nucleic acid extraction 210 is performed on a biological sample.Examples of biological samples that contain nucleic acids includesaliva, blood, fecal, and urine samples. To extract the nucleic acidsfrom the biological sample, other components of the cell must beinactivated and/or degraded. Nucleic acid extraction 210 can be carriedout by contacting the biological sample with an enzymatic mixture. Theenzymatic mixture can be a liquid-phase mixture. The enzymatic mixturecan enzymatically digest proteins and other cellular interferences inthe biological sample, with the exception of nucleic acids. In anembodiment, the enzymatic mixture includes thermostable proteinases. Thethermostable proteinases can be from thermophilic Bacillus species. Forexample, a liquid phase mixture including thermostable proteinases fromthermophilic Bacillus species is disclosed in U.S. Patent ApplicationPublication No. 2004/0197788, which is incorporated herein by referencein its entirety. In an embodiment, the enzymatic mixture performsnucleic acid extraction when a sample collection portion (e.g., in theform of a swab) of a sample acceptor holding a biological sample iscontacted by the enzymatic mixture. In an example, a final nucleic acidconcentration of the resulting extracted nucleic acid mixture is in arange of 0.5-20 ng/μL.

Nucleic acid extraction 210 can be followed by nucleic acidamplification 220 without additional treatment of the extracted nucleicacid mixture. Specifically, a portion of the extracted nucleic acidmixture can be mixed with amplification reagents to perform nucleic acidamplification 220 without additional purification steps. The enzymaticnucleic acid extraction procedure described herein can generatesufficiently clean nucleic acid solutions to proceed with amplification.The nucleic acid solutions may contain species that are sufficientlybroken down so that they do not interfere with subsequent reactions.

Nucleic acid amplification 220 can follow nucleic acid extraction 210.Nucleic acid amplification 220 is performed on template nucleic acidregions (sequences) in an extracted nucleic acid mixture. Nucleic acidamplification 220 can be performed by polymerase chain reaction (PCR),among other amplification techniques. To perform PCR, DNA having one ormore template regions is mixed with suitable PCR reagents. PCR reagentsinclude a DNA polymerase, nucleotides, and primers (oligonucleotides)that contain sequences complementary to the template DNA sequences. Thepolymerase enzymatically produces a new DNA strand from the template DNAby using the template DNA to guide synthesis of the new DNA strandthrough the extension of the primers by incorporating nucleotides at theend of the primers. The primers can be tagged with labels to generatelabeled synthesized DNA strands after amplification. In otherembodiments, the synthesized DNA strands can be tagged with labelsduring PCR by, for example, using labeled nucleotides to synthesize theDNA strands. The labels can be fluorescent labels. Fluorescents labelsemit fluorescence of known wavelengths when excited by a laser beam. PCRrequires thermal cycling. Thermal cycling is the repeated heating andcooling of the PCR mixture, including the PCR reagents and template DNA.Thermal cycling is conducted to melt the DNA, hybridize the primers tothe template DNA, and to perform enzymatic replication of the templateDNA regions. As PCR progresses, the DNA generated is itself used astemplate DNA for replication in succeeding cycles. Thus, PCR is a chainreaction that exponentially amplifies the template DNA regions.Amplification results in an amplified nucleic acid mixture.

Nucleic acid separation 230 can follow nucleic acid amplification 220.Nucleic acid separation 230 is performed to separate nucleic acidfragments in a nucleic acid mixture, such as an amplified nucleic acidmixture, and can enable detection and analysis of the nucleic acidfragments. In embodiments, electrophoresis can be used to separate thenucleic acid fragments by size. In electrophoresis, nucleic acidfragments are subjected to an electric field to force the nucleic acidfragments through a sieving medium. The nucleic acid fragments migrateby force of the electric field at different speeds based on size. Anelectric field induces a nucleic acid fragment to migrate due to the netnegative charge of the sugar-phosphate backbone of the nucleic acidfragment. The sieving medium can be a polymer matrix formed from apolymer solution. As examples for forming such a matrix, suitablepolymer solutions are disclosed in U.S. Pat. Nos. 8,207,258, 8,017,682,7,862,699, 7,531,073, 7,399,396, 7,371,533, 7,026,414, 6,811,977 and6,455,682, which are incorporated herein by reference in theirentireties. In an example, a sieving polymer matrix can be used to yieldsingle-base resolution. During or after separation, the DNA fragmentscan be detected and analyzed.

FIG. 3 shows exemplary features for performing nucleic acid extractionthat can be included within a microfluidic cartridge 300. As shown, themicrofluidic cartridge 300 can be provided with an extraction mixturereservoir 310 in fluid communication with a sample input 320. Otherfeatures for performing nucleic acid extraction may be providedoff-cartridge. In an embodiment, the off-cartridge features include asample acceptor 330 and an extraction thermal module 340. In an example,the sample acceptor 330 and the extraction thermal module 340 arecoupled together. The extraction mixture reservoir 310 is configured tohold the enzymatic mixture for performing nucleic acid extraction. Inembodiments, the extraction mixture reservoir is configured to hold fromabout 25 μl to about 500 μl, such as from about 200 μl to about 250 μlor about 225 μl, of the enzymatic mixture. The enzymatic mixture isprovided to or pre-loaded in the extraction mixture reservoir 310.

In use, the sample acceptor 330 is coupled with the sample input 320such that the extraction mixture reservoir 310, the sample input 320,and the sample acceptor 330 are in fluid communication. The sampleacceptor 330 presents a previously-collected biological sample fornucleic acid extraction. In embodiments, the minimal amount ofbiological material required to be presented is about 100 cells. Theenzymatic mixture can be provided from the extraction mixture reservoir310 to the sample acceptor 330 in order to initiate nucleic acidextraction. To aid enzymatic digestion, the enzymatic mixture can bemoved in a back-and-forth motion within the sample acceptor 330 and theextraction mixture reservoir 310. The extraction thermal module 340 canheat the enzymatic mixture to promote enzymatic digestion of cellularcomponents other than nucleic acids. Extraction can be performed at afirst temperature. Enzymes of the enzymatic mixture can be inactivatedat a second higher temperature to conclude nucleic acid extraction. Inan example, nucleic acid extraction is performed at 75° C. for 10minutes to extract the nucleic acids through enzymatic digestion. Then,the heat is increased and held at 95° C. to inactivate the enzymes inthe enzymatic mixture. In such an example, the enzymes includethermostable proteinases that functional at 75° C., but that areinactivated at higher temperatures, such as 95° C. Upon completion ofenzymatic digestion, the resulting extracted nucleic acid mixture can bereceived by and stored in the extraction mixture reservoir 310 forfurther processing. The extraction mixture reservoir 310 can have one ormore fluidic channels (not shown) branching from the extraction mixturereservoir 310 to provide the extracted nucleic acid mixture to otherportions of the microfluidic cartridge through a fluidic network.

FIGS. 4 and 5 show a plurality of exemplary sample acceptors 400fluidically coupled to a plurality of exemplary sample inputs 405 formedon an outer surface 410 of an exemplary microfluidic cartridge 415. Asshown, each sample input 405 includes a portion surrounding an openingthat protrudes from the outer surface 410 of the microfluidic cartridge415. In FIGS. 4 and 5, four sample acceptors 400 are fluidically coupledto four sample inputs 405 of the microfluidic cartridge 415. In otherembodiments, the microfluidic cartridge 415 can include less than foursample inputs 405, including a single sample input 405, or more thanfour sample inputs 405 for fluidically coupling the same number ofsample acceptors 400. The sample inputs 405, as well as the sampleacceptors 400, can be of the same or different types. As shown, thesample acceptors 400 and the sample inputs 405 are of the same type.Alternatively, one or more of the sample acceptors 400 and the sampleinputs 405 can be of different types.

As further shown, each sample acceptor 400 includes an input-matableportion 420, an acceptor portion 425, and a detachable portion 430 forsample collection. The input-matable portion 420 is at one end of theacceptor portion 425. The acceptor portion 425 is in the form of abarrel similar to a syringe barrel. The input-matable portion 420 can beconfigured to be coupled to the sample input 405 to form a fluid-tightseal. The input-matable portion 420 and the sample input 405 can bebased on any small-scale fluid fitting system. In embodiments, theinput-matable portion 420 and the sample input 405 each have a universalconnector selected from the group consisting of Luer-Lok connectors,threaded connectors, and flanged connectors. For example, theinput-matable portion 420 and the sample input 405 can be based on aLuer-Lok fitting system. In an embodiment, the sample input 405 isthreaded such as to be a female Luer-Lok fitting and the input-matableportion 420 is based on a complementary male Luer-Lok fitting that hasan inner flange configured to fit inside the opening of the sample input405 and a second outer flange that is threaded and configured to bescrew-fitted onto the threaded sample input 405.

The detachable portion 430 is configured to be removed from the acceptorportion 425 to collect a biological sample and again coupled to theacceptor portion 425 after collection of the biological sample has beencompleted. To effectuate removable coupling, the detachable portion 430includes a flanged grip 435. The flanged grip 435 can be configured tobe reversibly coupled to a complementary end of the acceptor portion425. Extending from the flanged grip 435 is an elongated member 440 thatincludes a sample collection portion 445. The sample collection portion445 can be in the form of a swab.

Nucleic acid extraction can be performed when the microfluidic cartridge415 is coupled to a pressure module of a nucleic acid analyzer. Thepressure module can provide positive and/or negative pressure to forcean enzymatic mixture from an extraction mixture reservoir of themicrofluidic cartridge 415 into the sample acceptor 400 in order toperform nucleic acid extraction on a biological sample presented by thesample acceptor 400. To aid enzymatic digestion, the pressure module,through positive and/or negative pressure, can move the enzymaticmixture in a back-and-forth motion within the sample acceptor 400 andthe extraction mixture reservoir of the microfluidic cartridge 415. Theflanged grip 435 of the sample acceptor 400 can be gas permeable topermit gas (e.g., air) to exit the sample acceptor 400. As shown, thesample acceptor 400 is made gas permeable by including openings 450defined in the flanged grip 435.

The microfluidic cartridge 415 can include a vent port in fluidcommunication with the extraction mixture reservoir, which can place thepressure module in serial fluid communication with the sample acceptor400 through the extraction mixture reservoir and the sample input 405.In embodiments, the pressure module applies positive and/or negativepressure to the distal end of the extraction mixture reservoir to forcea volume of the enzymatic mixture through the sample input 405 into thesample acceptor 400, where the enzymatic mixture can submerge thebiological sample presented on the sample collection portion 445 of thesample acceptor 400. The pressure module, under control of a controllermodule, can then force the enzymatic mixture and dissolved biologicalsample back into the extraction mixture reservoir. The pressure modulecan revert at least a major portion of the enzymatic/biological samplemixture back into the sample acceptor 400. This back-and-forth motioncan be continued by operation of the pressure module using positiveand/or negative pressure, such as pneumatic pressure, and discontinuedonce nucleic acid extraction is completed. The turbidity associated withthe back-and-forth motion can aid nucleic acid extraction and canproduce a well-mixed solution of extracted nucleic acids.

During nucleic acid extraction, the sample acceptor 400 can be coupledto an extraction thermal module of a nucleic acid analyzer. As discussedabove, the extraction thermal module can heat the enzymatic mixture topromote enzymatic digestion of cellular components (other than nucleicacids) of the biological sample presented by the sample acceptor 400.

FIG. 6 shows a portion of an exemplary nucleic acid analyzer 600 thatincludes an extraction thermal module 610. As shown, sample acceptors400 are received by the nucleic acid analyzer 600 such that they areoperably coupled to the extraction thermal module 610. The extractionthermal module 610 can heat the sample acceptors 400 by contact heating.

FIG. 7 shows exemplary features for performing nucleic acidamplification on template nucleic acid regions in an extracted nucleicacid mixture. As shown, on-cartridge features included within amicrofluidic cartridge 700 include an amplification reagent reservoir710, a mixing chamber 720, and an amplification chamber 730. In thisexample, the amplification reagent reservoir 710, the mixing chamber720, and the amplification chamber 730 are in serial fluidcommunication. However, other types of fluid communication are possible.The amplification reagent reservoir 710 holds amplification reagents forperforming a nucleic acid amplification reaction. In an embodiment, theamplification reagents are PCR reagents, including a DNA polymerase,nucleotides, and primers. The amplification reagents can be contained inmore than one amplification reagent reservoir 710. In an embodiment, theDNA polymerase is contained in a separate amplification reagentreservoir 710 from the primers and nucleotides.

During operation, the amplification reagents are provided to the mixingchamber 720. A portion of an extracted nucleic acid mixture is alsoprovided to the mixing chamber 720. In this embodiment, the extractednucleic acid mixture portion is provided to the mixing chamber 720 usingthe same fluidic channel as used to provide the amplification reagentsto the mixing chamber 720. In embodiments, the extracted nucleic acidmixture portion is from about 1 μl to about 50 μl, such as from about 25μl to about 35 μl or about 30 μl. The extracted nucleic acid mixtureportion can be mixed with the amplification reagents in a ratio of from0.1:1 to 1:1 or from 1:1 to 1:0.1 depending on the concentrations of thereagents. The total volume of the extracted nucleic acid mixture portionand the amplification reagents can be from about 25 μl to about 100 μl.The extracted nucleic acid mixture portion and the amplificationreagents can be prevented from mixing until they reach the mixingchamber 720 by moving the extracted nucleic acid mixture portion and theamplification reagents in discrete volumes. The discrete volumes can bephysically separated. For instance, because the extracted nucleic acidmixture portion and the amplification reagents are in liquid volumes,the liquid volumes can be kept physically separate by moving anotherfluid, such as air, in between the liquid volumes. In an alternativeembodiment, the extracted nucleic acid mixture portion can be providedto the mixing chamber using a different fluidic channel.

In the mixing chamber 720, the extracted nucleic acid mixture portioncontaining the extracted nucleic acids and the amplification reagentsare mixed. The mixing chamber 720 can hold a total solution volumegreater than the total solution volume to be introduced. This designallows space for air bubbles to rise from the fluid surface to the topof the chamber and the contained gas (e.g., air) can escape through afluidically-coupled vent. The dimensions of the mixing chamber 720 canbe further optimized for the escape of bubbles. For example, the ventcan be configured on the opposite end of an elongated, chamber from theinput channels where fluid is introduced. The input channels in fluidcommunication with the mixing chamber 720 may be in a perpendicularorientation to the long side of the mixing chamber 720 so as to promoteturbidity among the introduced fluids. In other words, the mixingchamber 720 can be configured to have a liquid mixing portion and a gasvent portion above the liquid mixing portion. The gas vent portion canbe above each fluidic channel in communication with the mixing chamber720. Each fluidic channel in communication with the mixing chamber 720can interface with the mixing chamber 720 at the bottom portion of themixing chamber 720 to prevent bubble development and generate a risingfluid level that pushes bubbles to the gas vent portion. In anembodiment, the mixing chamber 720 includes a hydrophobic surface thatrepels aqueous liquid away from the gas vent portion. Thus, thehydrophobic surface can protect against the extracted nucleic acidmixture portion or amplification reagents from entering or beingretained in the gas vent portion. The hydrophobic surface can functionas a barrier separating the liquid mixing portion and the gas ventportion. The hydrophobic surface can have non-uniform geometries,heights, levels, and/or areas on the mixing chamber surface.Alternatively, the hydrophobic surface can be uniform.

The extracted nucleic acid mixture portion and the amplificationreagents are provided to and mixed in the liquid mixing portion of themixing chamber 720 to obtain an amplification mixture. Using featuresdiscussed above, the mixing chamber 720 can be configured to disrupt thelaminar flow of the extracted nucleic acid mixture portion and theamplification reagents as they enter the mixing chamber 720. Laminarflow disruption can cause mixing of the amplification reagents and theextracted nucleic acid mixture portion to obtain the amplificationmixture. Gas, such as air, released during mixing of the extractednucleic acid mixture portion and the amplification reagents can bereleased from the liquid mixing portion to the gas vent portion of themixing chamber 720. From the gas vent portion, gas can be released fromthe microfluidic cartridge 700 though a channel in fluid communicationwith the mixing chamber 720. The fluidic channel for gas release can bea dedicated channel for this purpose or can be a non-exclusive channelthat is used for other purposes. A gas vent outlet can be at the end ofthe fluidic channel to allow the gas to escape into the environmentoutside the microfluidic cartridge 700. By venting gas, the mixingchamber 720 can protect against bubbles being present in theamplification mixture during further processing of the sample. Themixing chamber 720 is in fluid communication with the amplificationchamber 730.

The amplification chamber 730 is configured for nucleic acidamplification. In embodiments, the amplification chamber 730 is used toperform PCR. To perform PCR, the amplification chamber 730 can beconfigured for thermal cycling from an amplification thermal module 740.In an embodiment, the amplification thermal module 740 includes aheating unit configured to perform non-contact or contact heating. As anexample, the heating unit is an infrared light source for non-contactheating. The amplification thermal module 740 can include a temperaturesensing unit. In an embodiment, the temperature sensing unit is aninfrared pyrometer. To improve pyrometer sensing accuracy, theamplification chamber 730 can include a thinner portion for infraredpyrometer measurements. The infrared pyrometer measurements at thethinner portion can more accurately reflect the temperature of liquidwithin the amplification chamber 730. Thermal cycling requires cooling.Thus, the amplification chamber 730 can be configured through materialchoice to perform rapid cooling when not being heated. In suchembodiments, the amplification thermal module 740 does not need acooling unit to cool the amplification chamber 730. Alternatively, theamplification thermal module 740 can include a cooling unit to performcooling. As an example, the cooling unit is a cooling fan. In anotherembodiment, the cooling unit is a compressed air outlet.

During operation, the amplification mixture is provided to theamplification chamber 730. In embodiments, the amplification mixtureprovided to the amplification chamber 730 has a volume of from about 100μl to about 5 μl, such as from about 500 μl to about 1.5 μl or about 1μl. The amplification mixture can have laminar flow as it is provided tothe amplification chamber 730 from a fluidic channel exiting the mixingchamber 720. In the amplification chamber 730, the amplification mixtureis placed under reaction conditions to amplify template nucleic acidregions (sequences). As an example, the amplification mixture is thermalcycled to perform PCR. During amplification, the amplified nucleic acidscan be tagged with labels, such as fluorescent labels. Afteramplification, the resulting amplified nucleic acid mixture is availablefor further processing.

FIG. 8 shows exemplary features of a loadable reservoir that can beincluded within a microfluidic cartridge 800. As shown, the microfluidiccartridge 800 includes a reagent reservoir 805 that can be loaded with areagent solution for performing nucleic acid analysis. The reagentreservoir 805 can be configured to hold any of extraction,amplification, and separation reagents. For example, the reagentreservoir 805 is an amplification reagent reservoir as discussed above.The reagent reservoir 805 is in fluid communication with one or morefluidic channels 810 that lead to other portions of a fluidic network ofthe microfluidic cartridge 800. One or more (e.g., two) seals 815 arepositioned in the one or more (e.g., two) fluidic channels 810 to blockthe reagent solution from entering or prematurely entering otherportions of the fluidic network. The seals 815 can be non-reusable(one-time) or reusable seals and each seal 815 can be of a differenttype. In embodiments, the seals 815 are frangible seals that can bebroken by pressure supplied from a pressure module of a nucleic acidanalyzer. The seals 815 can be broken in order to move the reagentsolution to another portion of the fluidic network of the microfluidiccartridge 800 and/or to bring the reagent solution under hydrodynamiccontrol of a pressure module of a nucleic acid analyzer. Themicrofluidic cartridge 800 further includes one or more (e.g., two)bypass fluidic channels 820 in fluid communication with the reagentreservoir 805. The bypass fluidic channels 820 merge with the fluidicchannels 810 at junctions 825. A port 830 is in fluid communication witheach bypass channel 820 at the other end of the bypass channel 820. Oneof the ports 830 can be designated as a filling port and the other ofthe ports 830 can be designated as a gas outlet. At least the fillingport 830 can be configured to be fluidically coupled to an off-cartridgestore of the reagent solution to be loaded in the reagent reservoir 805.

The reagent reservoir 805 can be loaded with the reagent solution byproviding the reagent solution to the reagent reservoir 805 through oneof the ports 830 and the associated bypass fluidic channel 820. Gas(e.g., air) present in the reagent reservoir 805 (and the filling port830 and the associated bypass channel 820) that is displaced duringloading of the reagent solution can be expelled out of the reagentreservoir 805 through the other bypass fluidic channel 820 and theassociated gas outlet port 830. The gas outlet port 830 can be open tothe environment outside the microfluidic cartridge 800 during reagentloading to permit gas to be expelled from the microfluidic cartridge800. After loading, a sealing member (not shown), such as an adhesivefilm, can be placed over the ports 830 to protect against contamination.The sealing member can be air-permeable, but not liquid-permeable. Thesealing member can be hydrophobic. In embodiments, the sealing member ismade from a pressure-sensitive adhesive (PSA) polymer.

FIG. 9 shows exemplary features for performing nucleic acid separationthat can be included within a microfluidic cartridge 900. Theon-cartridge features include a separation channel 910. The separationchannel 910 can be filled with, for example, a sieving polymer matrix.The sieving polymer matrix can be formed by providing a sieving polymerto the separation channel 910 before nucleic acids are provided to theseparation channel 910 for separation. In an embodiment, a nucleic acidmixture, such as a portion of an amplified nucleic acid mixture, can beprovided to the separation channel 910. A high voltage module 920applies high voltage to electrodes (not shown) on the microfluidiccartridge 900 to induce electro-kinetic injection and/or electrophoreticseparation. As shown, a T-junction 930 is provided at the beginning ofthe separation channel 910. The nucleic acid mixture can be provided tothe beginning of the separation channel 910 by electro-kinetic injectionof a portion of the amplified nucleic acid mixture through a fluidicchannel 940.

Before being provided to the separation channel 910, the nucleic acidmixture (or a portion thereof) can be diluted or mixed with one or moreseparation reagent solutions, such as any of an internal controlsolution, a dilution solution, and a buffer solution, to improve nucleicacid separation. The nucleic acid mixture (or portion thereof) can bemixed with the separation reagents in a ratio of about 1:1 to about1:100, such as from about 1:10 to about 1:30 or about 1:15, depending onthe concentrations of the reagents. As an example, the nucleic acidmixture can be mixed with an internal control solution that includes aninternal lane standard (ILS). The ILS can be used to better ensureaccurate size measurements of the nucleic acid fragments. The ILSincludes nucleic acids of known size that are used as controls. Theinternal control solution can also include formamide for denaturingnucleic acids to promote separation. As another example, the nucleicacid mixture can be mixed with an aqueous dilution solution to reducethe ionic strength of the nucleic acid mixture. In order to detect andanalyze the separated nucleic acid fragments, the nucleic acid fragmentscan be labeled prior to separation. The nucleic acid fragments can belabeled during amplification, such as with fluorescent labels.Alternatively, the nucleic acid fragments can be labeled afteramplification but prior to separation by mixing the nucleic acidfragments with a dye, such as an intercalating dye (e.g., ethidiumbromide). The dye can be included in the internal control solution oranother solution.

Once the nucleic acid mixture, such as a portion of an amplified nucleicacid mixture mixed with separation reagents, is provided to theseparation channel 910, the nucleic acid fragments within the mixturecan be separated. In an embodiment, nucleic acid separation is performedby electrophoresis such that nucleic acid fragments are separated bysize. In electrophoresis, the nucleic acid fragments migrate by force ofthe electric field at different speeds based on the sizes of the nucleicacid fragments. During separation, the separated nucleic acid fragmentscan be detected through observation of the detection region 950 of theseparation channel 910. The detection region 950 can include a detectionwindow configured to enable detection by a laser beam. A detectionmodule 960 is operably coupled to the detection region 950. Thedetection module 960 can emit a laser beam. The laser beam can bedirected to the detection region 950 to excite fluorescent moleculesassociated with the nucleic acid fragments as they pass through thedetection region 950 during nucleic acid separation.

FIG. 10 shows an exemplary microfluidic cartridge 1000 and an exemplarysealing layer 1010 to be applied over at least a major portion of themicrofluidic cartridge 1000. Broadly, the microfluidic cartridge caninclude one or more sample inputs 1020, one or more fluidic networks1030, and one or more vent port areas 1040. As shown, four sample inputs1020, fluidic networks 1030, and vent port areas 1040 are defined in themicrofluidic cartridge 1000. The sample inputs 1020 can be configuredfor fluidic coupling of sample acceptors. The fluidic network 1030 caninclude features for performing any of nucleic acid extraction,amplification, and separation. Each vent port area 1040 includes aplurality of vent ports that can be configured for coupling to apressure module of a nucleic acid analyzer to provide hydrodynamiccontrol over liquid within the fluidic networks 1030 during nucleic acidanalysis.

The sealing layer 1010 is applied over at least the fluidic networks1030 of the microfluidic cartridge 1000 to provide a top layer overfluidic network features, including channels, reservoirs, and chambers.In embodiments, the sealing layer 1010 is applied over the sample inputs1020 and the fluidic networks 1030 or over the entirety of themicrofluidic cartridge 1000. The sealing layer 1010 can be in the formof a film and can be pliable. The sealing layer 1010 can be adhered tothe surface of the microfluidic cartridge 1000 by heat-drivenlamination. In an embodiment, there are two sealing layers that arerespectively applied over the top and the bottom of the microfluidiccartridge 100.

The pressure module of the nucleic acid can be configured toindependently apply positive and/or negative pressure to individual ventports to effectuate hydrodynamic movement in performing nucleic acidanalysis. Each vent port can be in fluid communication with a discretefeature in the fluidic network 1030 such as to control hydrodynamicmovement of liquid with respect to such feature. The vent ports can becoupled to the pressure module through a micro-to-macro interface. Thevent ports can be covered with a covering (not shown) that permits thepassage of gas (e.g., air) while preventing the passage of liquid. Asshown, the vent port areas 1040 are provided on one side of themicrofluidic cartridge 1000. Although not necessary, this can generallyprovide minimal complexity in the micro-to-macro interface with thepressure module of the nucleic acid analyzer. The sealing layer 1010 canalso be used to form frangible seals within the fluidic networks 1030.

FIG. 11 shows an exemplary frangible seal 1100. As shown, the frangibleseal 1100 is formed from a depression 1110 defined within a fluidicchannel 1120. The depression 1110 has a depth that is greater than thedepth of the fluidic channel 1120. However, the depression 1110 can havea depth that is less than the depth of an adjacent reagent reservoir orother chamber. A sealing layer portion 1130 is extended into thedepression 1110 such that the sealing layer portion 1130 contacts and isadhered to the base of the depression 1110.

The frangible seal 1100 can be configured to have a predeterminedresistance against fluid flow. Fluid flow resistance can be determinedby the depth and width of the depression 1110. In general, the frangibleseal 1110 has weaker fluid flow resistance as the depression 1110 ismade deeper and has greater fluid flow resistance as the depression 1110is made shallower. A shallower depression 1110 does not stretch thesealing layer portion 1130 as much as a deeper depression 1110 and,thus, a shallower depression 1110 provides more resistance to fluidflow. In embodiments, a fluidic network of a microfluidic cartridgeincludes frangible seals 1100 having different fluid flow resistances.

For instance, the fluidic network can have frangible seals 1100 thathave two different fluid flow resistances. A depression 1110 having adepth of about 40 μm to about 50 μm can be used to form frangible seals1100 that have sufficient fluid flow resistance to border reagentreservoirs to protect against reagent solution from entering otherportions of the fluidic network in the course of loading reagents oroperating the microfluidic cartridge until the frangible seals 1100 areintentionally broken by pressure applied by a pressure module. Adepression 1110 having a depth of about 15 μm to about 25 μm can be usedto form a frangible seal 1100 having a greater fluid flow resistance.The frangible seal 1100 of greater fluid flow resistance can be used inplaces along the fluidic network where another actuation feature underthe control of the pressure module, such as a reusable actuation feature(e.g., a valve), is in close proximity to the location for the frangibleseal 1100 of greater fluid flow resistance. A frangible seal 1100 ofgreater fluid flow resistance is provided in such places to protectagainst inadvertent seal breakage during operation of the actuationfeature.

During operation of the microfluidic cartridge, the frangible seal 1100can be broken by providing positive or negative pressure of sufficientforce through the fluidic channel 1120. Such pressure can cause thesealing layer portion 1130 to detach from the base of the depression1110. One detached, the sealing layer portion 1130 does not normallyreattach to the depression 1110 once pressure is removed. Thus, oncebroken, the frangible seal 1100 is not automatically reconstituted andrepresents a one-time actuation feature of the microfluidic cartridge.

FIG. 12 shows a schematic of an exemplary microfluidic cartridge 1200that combines various features for nucleic acid extraction, nucleic acidamplification, and nucleic acid separation. The microfluidic cartridge1200 includes four identical nucleic acid analysis portions 1210, inwhich a biological sample can be analyzed. Accordingly, the nucleic acidanalysis may be performed on four different biological samples inparallel or in tandem. In other embodiments, the microfluidic cartridge1200 can include more or less nucleic acid analysis portions and mayonly contain a single nucleic acid analysis portion 1210. However, theincorporation of more than one nucleic acid analysis portion 1210 on amicrofluidic cartridge 1200 can improve efficiency and/or convenience.Of course, different biological samples can be individually analyzed inthe nucleic acid analysis portions 1210. Alternatively, a biologicalsample can be divided and nucleic acid analysis performed more than onceon the same biological sample. Such redundancy can improve accuracy.Further, there is no requirement that all nucleic acid analysis portions1210 are identical as, for example, nucleic acid analysis portions 1210on the microfluidic cartridge 1200 can be configured to performdifferent types of nucleic acid analyses. Alternatively, the individualnucleic acid analysis portions 1210 may be used to perform analyses onunknown samples, positive control samples, negative control samples, orany combination thereof. For instance, a first nucleic acid analysisportion 1210 can be used to analyze an unknown sample and a secondnucleic acid analysis portion 1210 can be used to analyze an allelicladder.

The cartridge interface module (CIM) is designed to connect to andcontrol a disposable or interchangeable microfluidic cartridge, such asthat described in U.S. patent application Ser. No. 13/064,094, which isincorporated in its entirety by reference herein. The microfluidiccartridge is inserted into the CIM and utilized in a user friendlymanner without the possibility of instrument or human contamination forDNA identification. The CIM allows for a microfluidic cartridge to beinserted into an opening that guides it to the correct loading area.When a door of the nucleic acid analyzer system is closed, the systemlocks both the door in place and engages the CIM. When the CIM isengaged, the microfluidic cartridge becomes linked to the instrument,which allows for a DNA identification test to be run. When the testingis completed, the CIM disengages from the microfluidic cartridge and thedoor is unlocked.

FIG. 13 illustrates an exemplary CIM 1300, which includes an upperportion 1301 and a lower portion 1302, and an intervening slot 1303 inwhich a removable microfluidic cartridge 1305 is inserted and removed.The cartridge 1305 can rest on a metal plate of a stage. On the upperportion 1301, a high voltage electrode component 1310 is illustrated.The high voltage electrode component 1310 provides an automaticconnection of high voltage sources directly to microfluidic channels onthe cartridge 1305, while maintaining a fluidic seal of the cartridge1305. In contrast, some conventional systems insert electrodes into thecartridge.

A microfluidic valve actuator component 1320 is also illustrated in FIG.13. The microfluidic valve actuator component 1320 seals the cartridge1305 to the CIM 1300. A pneumatic connector component 1330 is alsoillustrated in FIG. 13, which provides a contamination-proof fluidicseal to the cartridge 1305 from the rest of the system. Someconventional systems require replacement of direct fluid connectionsafter each test since the DNA from a previous test can contaminate theresults of later tests. Embodiments described herein for a pneumaticconnector component 1330 provide a contamination-free environment forcontinuous testing without changing out any parts.

A cartridge support component 1340, illustrated in FIG. 13 provides thecartridge 1305 with structural support. The embodiment described hereinprovides a CIM 1300 to be used in conjunction with a removable plasticcartridge 1305. The cartridge support component 1340 provides support tothe cartridge 1305, which allows much greater forces to be applied tothe cartridge 1305. The combination of pneumatic connections, cartridgesupporting structures, and mechanical microfluidic valve actuators areconfigured in the CIM 1300 to reduce or eliminate the possibility ofcross contamination.

FIG. 13 further illustrates a fluidics component 1350, which directs apressure source to the cartridge 1305. The embodiment of the CIM 1300directs flow from four or more pressure sources to twenty four or moreports on the microfluidic cartridge 1305. This provides a fluid movementon a microfluidic scale to drive the fluid through a test, while alsoproviding design flexibility to optimize the flow characteristics. Astage heater component 1360 on the lower portion 1302 of the CIM 1300uniformly heats the cartridge 1305. A liquid extraction heater component1370 on the upper portion 1301 of the CIM 1300 works in conjunction withthe fluidics component 1350 to initiate and support a simplifiedextraction analysis process in the microfluidic cartridge 1305 withreduced cross contamination. The liquid extraction heater component 1370supports a fully integrated liquid-based extraction, which allows DNAextraction with a limited control system and less complexity than asolid phase extraction process used in some conventional processing.Solid phase extraction uses metallic beads to extract the DNA from thecells that need to be processed, washed, and removed. In contrast,liquid phase extraction uses an enzyme to extract the DNA, which onlyrequires the aliquot to be thermo-cycled. This greatly simplifies theoverall system.

A PCR assembly component 1380, illustrated in FIG. 13, initiates andsupports the amplification process in the microfluidic cartridge 1305.The PCR component 1380 utilizes a non-contact infrared thermo-cyclingprocess, which is described below with reference to FIG. 15.

A detection optics component 1390 of the CIM 1300 is also shown in FIG.13. The detection optics component 1390 and the high voltage electrodescomponent 1310 work in conjunction in a nucleic acid separation process.The separation process is achieved by utilizing a shorter separationchannel within the microfluidic cartridge. For example, an embodiment, achannel of approximately 7 cm is used. Embodiments described hereinutilize a microfluidic chip architecture, rather than require anadditional sub-assembly to the system to execute the separation process.In some conventional systems that require a separate sub-assembly, thegenetic material to be tested is passed from the microfluidic cartridgeinto the testing instrument. In contrast, embodiments described hereinprovide a microfluidic chip-based electrophoresis component. The shorterseparation channel utilized by the microfluidic chip architecture,together with the pneumatic connections, cartridge supportingstructures, and mechanical microfluidic valve actuators in the CIM 1300reduce or eliminate the possibility of cross contamination frominstrument contamination and human intervention. This is made possibleby eliminating the need to move the genetic material to be tested fromthe microfluidic cartridge into a separate sub-assembly.

FIG. 14 is a drawing which illustrates a top view and a side view of anembodiment of a cartridge interface module 1400. A high voltageelectrode 1410 provides a high voltage source directly to themicrofluidic channels on a cartridge. The fluidic seal of the cartridgeis maintained. A cartridge 1420 is also illustrated. In an embodiment,the cartridge 1420 is removable and disposable, and subsequentcartridges can easily be swapped and inserted for subsequent testing. Afluidics region 1430 directs flow from multiple pressure sources tomultiple ports on the microfluidic cartridge 1420. A CIM actuator 1440seals the system from the inserted cartridge 1420. A pneumatic connector1450 provides a contamination-proof fluidic seal to the cartridge 1420from the rest of the system. A cartridge support 1460 provides thecartridge 1420 with structural support. The PCR assembly 1470 providesnon-contact infrared thermo-cycling. A stage heater 1480 uniformly heatsthe cartridge 1420.

FIG. 14 also illustrates an optical device assembly 1490. In anembodiment, an optical device provides an illuminating path that directsa first input light beam received from a light source to a firstseparation channel of a microfluidic chip. The first input light beamcauses fluorescent labels attached onto DNA fragments in the firstseparation channel to emit a first fluorescence light. A detecting pathcollects and directs the first fluorescent light to a first group ofoptical fibers. A spectrometer receives the first fluorescent light fromthe optical fibers and detects fluorescent components in the firstfluorescent light. Additional embodiments of the optical device assembly1490 are further described in U.S. patent application Ser. No.13/273,947, which is incorporated by reference herein in its entireties.

Referring back to FIG. 13, the PCR component 1380 of the CIM 1300utilizes complete non-contact nucleic acid amplification processing. Aninfrared wavelength can be used to heat liquid in the PCR chamber of themicrofluidic cartridge. In addition, a non-contact temperature sensorcan be used, such as a pyrometer. FIG. 15 illustrates a top view and aside view of a pyrometer 1500 used in conjunction with a nucleic acidanalyzer system, according to embodiments described herein. A pyrometerassembly 1510 is positioned above the CIM. An infrared source 1520 isdirected towards a cartridge 1530. Other temperature sensors arecontemplated by embodiments described herein, in which a non-contactmethod and system intercept and measure thermal radiation.

The CIM of a nucleic acid analyzer system described herein provides aninterface to receive a removable microfluidic cartridge, containing allneeded reagents and samples, and provide all needed functionality to themicrofluidic cartridge for nucleic acid extraction, amplification, andseparation. The CIM has several advantages and features, including butnot limited to a user-friendly cartridge input, a liquid extractionheater and feedback, a stage heater and feedback, an integratedmicrofluidic control, integrated microfluidic valve mechanics, acartridge support, a PCR cycling apparatus, a microfluidic chip basedelectrophoresis apparatus, contamination-free pneumatic connections, anda modular design for ease of servicing.

FIG. 16 is a flow diagram illustrating an exemplary process 1600 ofanalyzing a biological sample for DNA analysis. A removable microfluidiccartridge is received into a cartridge interface module (CIM) of anucleic acid analyzer system in step 1610. An extraction of nucleicacids from the biological sample contained within the removablemicrofluidic cartridge is initiated and supported, via a fluidicscomponent of the CIM while engaged with the removable microfluidiccartridge in step 1620. An amplification of the extracted nucleic acidsis initiated and supported, via a polymerase chain reaction (PCR)assembly component of the CIM while engaged with the removablemicrofluidic cartridge in step 1630. A separation of the amplifiednucleic acids into nucleic acid fragments is initiated and supported,via a high voltage electrodes component of the CIM, while engaged with aseparation channel of the removable microfluidic cartridge in step 1640.An input light beam is directed to a separation channel for detectionand collection of the nucleic acid fragments, via a detection opticscomponent of the CIM in step 1650. The CIM is configured to integratewith a microfluidic chip architecture while engaged with the removablemicrofluidic cartridge for execution of the extraction, amplification,and separation of the biological sample within the removablemicrofluidic cartridge.

While the invention has been described in conjunction with the specificexemplary embodiments thereof, it is evident that many alternatives,modifications, and variations will be apparent to those skilled in theart. Accordingly, exemplary embodiments as set forth herein are intendedto be illustrative, not limiting. There are changes that may be madewithout departing from the spirit and scope of the invention.

What is claimed:
 1. A cartridge interface module (CIM), configured toengage with a removable microfluidic cartridge in a nucleic acidanalyzer system, the CIM comprising: a fluidics component configured toinitiate and support a liquid extraction of nucleic acids from abiological sample contained in the removable microfluidic cartridge; apolymerase chain reaction (PCR) assembly component configured toinitiate and support amplification of the extracted nucleic acids; ahigh voltage electrodes component, configured to initiate and supportseparation of the amplified nucleic acids into nucleic acid fragments ina separation channel of the removable microfluidic cartridge; and adetection optics component, configured to detect labeled nucleic acidfragments, wherein the CIM is configured to integrate with amicrofluidic chip architecture of an inserted removable microfluidiccartridge for execution of the extraction, amplification, and separationof the biological sample within the removable microfluidic cartridge. 2.The CIM of claim 1, wherein the separation channel is integrated withthe microfluidic chip architecture.
 3. The CIM of claim 1, whereingenetic material from the biological sample is not transferred out ofthe removable microfluidic cartridge during analysis of the biologicalsample.
 4. The CIM of claim 1, further comprising: one or more pneumaticconnections within the CIM, configured to engage with the removablemicrofluidic cartridge.
 5. The CIM of claim 1, further comprising: oneor more cartridge supporting structures within the CIM that areconfigured to engage with the removable microfluidic cartridge.
 6. TheCIM of claim 1, further comprising: one or more mechanical microfluidicvalve actuators within the CIM that are configured to engage with theremovable microfluidic cartridge.
 7. The CIM of claim 1, wherein the PCRassembly component utilizes a non-contact mechanism to initiate andsupport the amplification of the extracted nucleic acids.
 8. The CIM ofclaim 7, wherein the non-contact mechanism comprises an infrared (IR)wavelength configured to heat liquid for the amplification.
 9. The CIMof claim 7, wherein the non-contact mechanism comprises a pyrometertemperature sensor.
 10. A method of analyzing a biological sample forDNA analysis, comprising: receiving a removable microfluidic cartridgeinto a cartridge interface module (CIM) of a nucleic acid analyzersystem; initiating and supporting extraction of nucleic acids from thebiological sample contained within the removable microfluidic cartridge,via a fluidics component of the CIM while engaged with the removablemicrofluidic cartridge; initiating and supporting amplification of theextracted nucleic acids, via a polymerase chain reaction (PCR) assemblycomponent of the CIM while engaged with the removable microfluidiccartridge; initiating and supporting separation of the amplified nucleicacids into nucleic acid fragments, via a high voltage electrodescomponent and a detection optics component of the CIM while engaged witha separation channel of the removable microfluidic cartridge; anddirecting an input light beam to a separation channel for detection andcollection of the nucleic acid fragments, via a detection opticscomponent, wherein the CIM is configured to integrate with amicrofluidic chip architecture while engaged with the removablemicrofluidic cartridge for execution of the extraction, amplification,and separation of the biological sample within the removablemicrofluidic cartridge.
 11. The method of claim 10, wherein theextraction occurs via a liquid-based process.
 12. The method of claim10, wherein the separation channel is integrated with the microfluidicchip architecture.
 13. The method of claim 10, wherein the amplificationincludes heating a liquid, via an infrared (IR) wavelength.
 14. Themethod of claim 13, wherein the amplification includes measuring atemperature of the liquid, via a pyrometer temperature sensor.
 15. Themethod of claim 10, wherein genetic material from the biological sampleis not transferred from the microfluidic cartridge during analysis ofthe biological sample.
 16. A cartridge interface module (CIM) of anucleic acid analyzer system, comprising: a fluidics component; a highvoltage electrode component; a pneumatic connector component; acartridge support component; a microfluidic valve actuator component; aliquid extraction heater component; a detection optics component; astage heater component; and a polymerase chain reaction (PCR) component,wherein the components of the CIM are configured to integrate with amicrofluidic chip architecture of an inserted removable microfluidiccartridge to extract, amplify, and separate a biological sample withinthe removable microfluidic cartridge.
 17. The CIM of claim 16, whereinthe fluidics component is configured to initiate and support liquidextraction of nucleic acids from the biological sample contained withinthe removable microfluidic cartridge engaged with the CIM.
 18. The CIMof claim 17, wherein the PCR component is configured to initiate andsupport amplification of the liquid-extracted nucleic acids, via anon-contact mechanism.
 19. The CIM of claim 18, further comprising: amicrofluidic chip architecture within the removable microfluidiccartridge integrated with the CIM.
 20. The CIM of claim 19, wherein themicrofluidic chip architecture integrated with the CIM is configured toseparate the amplified nucleic acids into nucleic acid fragments in aseparation channel of the removable microfluidic cartridge engaged withthe CIM.
 21. A cartridge interface module (CIM), configured to engagewith a pressure module in a nucleic acid analyzer system, the CIMcomprising: a pneumatic connector component, configured to providepositive and negative pressures from multiple sources of the pressuremodule to multiple vent ports of an inserted microfluidic cartridge; afluidics component, configured to direct pressure flow from the multiplesources to the multiple vent ports; a microfluidic valve actuatorcomponent; and a cartridge support component, wherein the components ofthe CIM are configured to integrate with a microfluidic chiparchitecture of the inserted microfluidic cartridge to extract, amplify,and separate a biological sample within the inserted microfluidiccartridge.
 22. The CIM of claim 21, wherein the pressure module connectsa solenoid manifold to the multiple vent ports of the insertedmicrofluidic cartridge, via one or more pneumatic connections.
 23. TheCIM of claim 21, wherein genetic material from the biological samplecontained within the inserted microfluidic cartridge is not transferredout of the inserted microfluidic cartridge during analysis of thebiological sample.
 24. The CIM of claim 21, wherein the pressure moduleis configured to effectuate hydrodynamic movement via pneumatic pressurein the inserted microfluidic cartridge.
 25. The CIM of claim 21, whereinthe pressure module is configured to actuate one or more valves withinthe inserted microfluidic cartridge.